The full lab begins with a friendly competition

Well, this was an exciting day. It started out with the arrival of the full lab. Travis and John began working at 9am this morning and quickly got busy reading for their various projects while I worked on preparing samples. (For the record, Travis was given the Nucleosome Packing project while John has been assigned to the DNA Liquid Crystal experiment.) I had a heck of a time getting the calibration solutions prepared as when I was ordering I neglected to buy a funnel for pouring solutions from a centrifuge tube to a volumetric flask. A little bit of begging over at chemistry and the help of Prof. Shelli Frey and I finished the job just a few minutes into lunch.

It was important that I finished these calibration solutions as they were needed for the afternoon competition. Basically, the idea was that Travis and John would make five solutions using their best pipetting skills. This activity had two purposes: One was to give Travis and John a chance to practice said skills. Pipetting is something that is quite easy to do but takes some skill to do right. The second and more important purpose was to see how well we could all pipette solutions and how well the machine could measure the concentrations of the various solutions.

Here are the results:

Where the highlighted values are the predicted values. Everyone did pretty well. Travis knew he had a bit of an issue when all of his volumes were a bit high, but look at that precision. John seemed right on for the most part. What concerns me more, however is how poorly even the John and my values match the predicted value.

One issue is that these samples were originally meant to be diluted by 10x. We’ll try that tomorrow. I’m also planning on changing the pump tubes out and trying to take more replicates. We eventually want an accuracy of ~1%.

The Adventures of T-Money

Today we took a tour of the lab and were shown most of the equipment that we would be using over the summer. We then started to read information about the projects that we would be working on. My readings focused on DNA and how the coils of DNA are wrapped around a hockey puck which is made up of two of each of the histones H2A H2B H3 H4. The histones are identical in size and fit together to form a hockey puck shape which the DNA is wrapped around twice before continuing on to another puck. This allows the long strand of DNA to be tightly compacted. At the top where the DNA comes off the puck is an H1 histone which serves as some sort of paperclip but I don’tknow the specifics of it yet. Now this configuration of DNA and histones is called the nucleosome. This is what transcription which is where some kinda genetic scanner scans a part of the DNA and then prints out a 3 piece copy of RNA which travels to proteins and fits into specific ones to activate them. I read about Transcription control which is controlling what part of the DNA gets scanned but did not read much farther into it. I also read a little about Histone Acetylation which is adding a specific acetyl group to the amino acids of the histone proteins causing the histone to loosen its grip on the DNA. We then went into the lab and practiced with the Micro Pipette creating 5 solutions of Co P Mg and de-ionized water and then testing our accuracy with the Spectrometer. The results showed that i either added a bit too much of each solution or added too much water but john later admit that he sabotaged my solutions.

June 7th

Today, after an overview and tour of the lab, we started out reading relevant research articles. The article I was reading was titled “DNA Inspired Electrostatics” by Gelbart, Bruinsma, Pincus and Parsegian. This article starts with a rough overview of DNA’s characteristics and behaviors. It takes the form of a disordered coil in physiological conditions, but when polyvalent cations are introduced, it forms a tightly packed torus. Polyvalent counterions cause an attraction between charged DNA molecules that would repel under normal conditions. The electrostatics that govern these counterion-meditated attractions are still being refined, but there are two mechanisms being studied. One is a Gaussian fluctuation correction to the PB mean-field theory, which treats the counterion cloud around each rod as a one-dimensional ideal gas. It is longer range and more effective at high temps. The other mechanism is a short range electrostatic correlations between the counterions of the two clouds. This is more effective at lower temperatures. The dense cloud of counterions surrounding DNA also represents a large number of hidden degrees of freedom.

In the afternoon, we worked with preparing a few test solutions. We created 5 different solutions with varying concentrations of Magnesium. All five solutions had constant concentrations of 1mM Co and 5mM P. Solutions 1-5 had concentrations of 0mM, 10mM, 12mM, 15mM, 17mM, respectively. We also performed the appropriate calculations to prepare these solutions. After preparing the solutions with Micro Pipettes, we learned how to operate and calibrate the spectrometer. We aligned the spectrometer first, and then used three known solutions to calibrate it. Once it was calibrated, we put through the test solutions that we made. My concentration results were fairly consistent with the predicted values, and due to the fact that I sabotaged Travis’s results, they were precise but rather inaccurate.

Making mistakes allows time for posting to the blog

I want this blog to be an informal collection of information related to my research lab and so I’ll start it about as informally as possible.

The reason I am able to post right now is because I have made a large mistake with the machine. I failed to connect the peristaltic pump tube correctly (specifically the outlet, or red, tube). This caused the spray chamber to be filled with liquid which eventually (thankfully) extinguished the plasma. I was in the room the entire time, ignoring everything that was going wrong. I will have to see if I can set the software to make a loud sound when things go wrong.

To recover, I started the pump back up on “flush” mode (which is simply a fast pumping mode) and waited for it to drain. When it finished draining, I started the plasma back up. The plasma extinguished quickly after igniting, but I was able to reignite it and it has (as of writing) been lit for about 10 minutes. When 30 minutes has passed, I’ll start to align the plasma, calibrate, and run my new “Mix” series of samples.

(Note: Relevant page of notebook is 35.)